Probabilities of the states at the base of the left descendant branch
Rcpp_rightprobs
Probabilities of the states at the base of the right descendant branch
COO_weights_columnar
Transition probability matrix in COO-like format as 4 columns:
ancestral index, left index, right index, conditional probability given ancestral states.
(assuming likelihood of descendants is 1). Indexes are 0-based.
Keep in mind that cladogenesis matrices exclude the null state
(a range of 0 areas), so if your states list starts with the
null range (as is typical/default in DEC-style models)
then to get the R 1-based state indices requires e.g.
COO_weights_columnar[[1]] + 2.
Rsp_rowsums
A vector of size (numstates) giving the sum of the relative probabilites of
each combination of descendant states, assuming the probabilities of the left- and right-states are
all equal (set to 1). This is thus the sum of the weights, and dividing by this normalization vector
means that the each row of the speciation probability matrix will sum to 1. Default assumes the
weights sum to 1 but this is not usually the case. Rsp_rowsums need only be calculated once per
tree+model combination, stored, and then re-used for each node in the tree, yielding significant
time savings.
printmat
Should the probability matrix output be printed to screen? (useful for debugging, but
can be dramatically slow in R.app for some reason for even moderate numbers of states; perhaps
overrunning the line length...)
Value
splitlikes Vector of the probabilities of each allowed split
# NOT RUN {# For the basic logic of a probablistic cladogenesis model, see?rcpp_calc_anclikes_sp
# For examples of running the functions, see the comparison of all functions at:# ?cladoRcpp# }